Reproductive performance of a cohort of Standardbred mares under a commercial breeding system

Background: Despite being a large commercial breeding industry, there is little published data on the reproductive success of Standardbred mares. Objectives: To quantify the reproductive performance of Standardbred mares under artificial breeding systems in a commercial setting and determine the incidence of early embryonic and other pre-partum losses. Study design: Retrospective cohort study. Methods: Data from four commercial farms were collected across four breeding years, and all mares were bred via artificial insemination. A total of 3995 mares contributed 7229 mare years. First-cycle pregnancy rate (FCPR) and end of season pregnancy rate (SPR) were analysed in mixed-effects logistic regression models. Time-to-conception interval was analysed in a Cox regression model. Results: The mean FCPR was 61.4% (confidence interval [CI] 60.3%–62.6%), the mean end of SPR was 84.7% (CI 83.8–85.5%), the mean live foal rate (FR) was 73.1% (CI 72.1%–74.2%). Mares located on-farm were more probable to be pregnant in terms of both FCPR (odds ratio [OR] 1.168, CI 1.018–1.340, p = 0.026) and SPR (OR 2.026, CI 1.673–2.454, p < 0.001), mares inseminated with thawed–frozen semen were less probable to be pregnant in terms of FCPR (OR 0.598, CI 0.457–0.783, p < 0.001) and SPR (OR 0.479, CI 0.354–0.647, p < 0.001) compared with insemination with fresh-extended semen. Older mares (14 years and older) were less probable to be pregnant in terms of FCPR (OR 0.795, CI 0.688–0.919, p = 0.002) and SPR (0.435, CI 0.352–0.538, p < 0.001) compared with young mares (3- to 8-year old). Main limitations: Retrospective data relied on accurate record keeping of stud farms and no mare-treatment or ovulation induction records were available. Live FRs relied mostly on annual foaling returns so fetal/foal deaths may be underrepresented. Conclusion: This study provides substantial baseline data on reproductive performance for Standardbred mares managed under a commercial artificial breeding system

Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes

BACKGROUND: Comparisons between the genomes of the closely related nematodes Caenorhabditis elegans and Caenorhabditis briggsae reveal high rates of rearrangement, with a bias towards within-chromosome events. To assess whether this pattern is true of nematodes in general, we have used genome sequence to compare two nematode species that last shared a common ancestor approximately 300 million years ago: the model C. elegans and the filarial parasite Brugia malayi. RESULTS: An 83 kb region flanking the gene for Bm-mif-1 (macrophage migration inhibitory factor, a B. malayi homolog of a human cytokine) was sequenced. When compared to the complete genome of C. elegans, evidence for conservation of long-range synteny and microsynteny was found. Potential C. elegans orthologs for II of the 12 protein-coding genes predicted in the B. malayi sequence were identified. Ten of these orthologs were located on chromosome I, with eight clustered in a 2.3 Mb region. While several, relatively local, intrachromosomal rearrangements have occurred, the order, composition, and configuration of two gene clusters, each containing three genes, was conserved. Comparison of B. malayi BAC-end genome survey sequence to C. elegans also revealed a bias towards intrachromosome rearrangements. CONCLUSIONS: We suggest that intrachromosomal rearrangement is a major force driving chromosomal organization in nematodes, but is constrained by the interdigitation of functional elements of neighboring genes

Student Knowledge of Signs, Risk Factors, and Resources for Depression, Anxiety, Sleep Disorders, and Other Mental Health Problems on Campus

A mixed methods study sought to assess student knowledge of signs, risk factors, and campus services available for mental health disorders. A survey was completed by 831 students and three focus groups were conducted. Respondents felt more knowledgeable about depression than about anxiety and sleep disorders. Graduate students and seniors had a keener awareness of risk factors for anxiety and sophomores were in the greatest danger of failing to recognize these risks. Males often failed to recognize signs and risk factors for mental health problems. Support groups, courses, and workshops on managing relationships, transition to college, and specific mental health disorders are advocated

Angular sensitivity of blowfly photoreceptors: intracellular measurements and wave-optical predictions

The angular sensitivity of blowfly photoreceptors was measured in detail at wavelengths λ = 355, 494 and 588 nm. The measured curves often showed numerous sidebands, indicating the importance of diffraction by the facet lens. The shape of the angular sensitivity profile is dependent on wavelength. The main peak of the angular sensitivities at the shorter wavelengths was flattened. This phenomenon as well as the overall shape of the main peak can be quantitatively described by a wave-optical theory using realistic values for the optical parameters of the lens-photoreceptor system. At a constant response level of 6 mV (almost dark adapted), the visual acuity of the peripheral cells R1-6 is at longer wavelengths mainly diffraction limited, while at shorter wavelengths the visual acuity is limited by the waveguide properties of the rhabdomere. Closure of the pupil narrows the angular sensitivity profile at the shorter wavelengths. This effect can be fully described by assuming that the intracellular pupil progressively absorbs light from the higher order modes. In light-adapted cells R1-6 the visual acuity is mainly diffraction limited at all wavelengths.

An evaluation of GO annotation retrieval for BioCreAtIvE and GOA

from A critical assessment of text mining methods in molecular biolog

Whither Capitalism? Financial externalities and crisis

As with global warming, so with financial crises – externalities have a lot to answer for. We look at three of them. First the financial accelerator due to ‘fire sales’ of collateral assets -- a form of pecuniary externality that leads to liquidity being undervalued. Second the ‘risk- shifting’ behaviour of highly-levered financial institutions who keep the upside of risky investment while passing the downside to others thanks to limited liability. Finally, the network externality where the structure of the financial industry helps propagate shocks around the system unless this is checked by some form of circuit breaker, or ‘ring-fence’. The contrast between crisis-induced Great Recession and its aftermath of slow growth in the West and the rapid - and (so far) sustained - growth in the East suggests that successful economic progress may depend on how well these externalities are managed

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

Motivation: Artemis and Artemis Comparison Tool (ACT) have become mainstream tools for viewing and annotating sequence data, particularly for microbial genomes. Since its first release, Artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory biologists and professional annotators. Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files. Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences

AgBase: a functional genomics resource for agriculture

BACKGROUND: Many agricultural species and their pathogens have sequenced genomes and more are in progress. Agricultural species provide food, fiber, xenotransplant tissues, biopharmaceuticals and biomedical models. Moreover, many agricultural microorganisms are human zoonoses. However, systems biology from functional genomics data is hindered in agricultural species because agricultural genome sequences have relatively poor structural and functional annotation and agricultural research communities are smaller with limited funding compared to many model organism communities. DESCRIPTION: To facilitate systems biology in these traditionally agricultural species we have established "AgBase", a curated, web-accessible, public resource for structural and functional annotation of agricultural genomes. The AgBase database includes a suite of computational tools to use GO annotations. We use standardized nomenclature following the Human Genome Organization Gene Nomenclature guidelines and are currently functionally annotating chicken, cow and sheep gene products using the Gene Ontology (GO). The computational tools we have developed accept and batch process data derived from different public databases (with different accession codes), return all existing GO annotations, provide a list of products without GO annotation, identify potential orthologs, model functional genomics data using GO and assist proteomics analysis of ESTs and EST assemblies. Our journal database helps prevent redundant manual GO curation. We encourage and publicly acknowledge GO annotations from researchers and provide a service for researchers interested in GO and analysis of functional genomics data. CONCLUSION: The AgBase database is the first database dedicated to functional genomics and systems biology analysis for agriculturally important species and their pathogens. We use experimental data to improve structural annotation of genomes and to functionally characterize gene products. AgBase is also directly relevant for researchers in fields as diverse as agricultural production, cancer biology, biopharmaceuticals, human health and evolutionary biology. Moreover, the experimental methods and bioinformatics tools we provide are widely applicable to many other species including model organisms